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Merge pull request #114 from common-workflow-language/draft-4.dev3-to-v1.0.dev4
[WIP] Draft 4.dev3 to v1.0.dev4
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290 files changed

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‎cwltool/process.py

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -89,7 +89,9 @@ def get_schema(version):
8989
return SCHEMA_CACHE[version]
9090

9191
cache = {}
92-
version = version.split("#")[-1].split(".")[0]
92+
version = version.split("#")[-1]
93+
if 'dev' in version:
94+
version = ".".join(version.split(".")[:-1])
9395
for f in cwl_files:
9496
try:
9597
res = resource_stream(__name__, 'schemas/%s/%s' % (version, f))
@@ -314,13 +316,13 @@ def __init__(self, toolpath_object, **kwargs):
314316

315317
global SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY # pylint: disable=global-statement
316318
if SCHEMA_FILE is None:
317-
get_schema("draft-4")
319+
get_schema("v1.0")
318320
SCHEMA_ANY = cast(Dict[unicode, Any],
319-
SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/salad#Any"])
321+
SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"])
320322
SCHEMA_FILE = cast(Dict[unicode, Any],
321-
SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#File"])
323+
SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"])
322324
SCHEMA_DIR = cast(Dict[unicode, Any],
323-
SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#Directory"])
325+
SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#Directory"])
324326

325327
names = schema_salad.schema.make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY],
326328
schema_salad.ref_resolver.Loader({}))[0]

‎cwltool/schemas/site/cwlsite-draft4-job.json

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@
4343
"https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement",
4444
"https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement",
4545
"https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement",
46-
"https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement",
46+
"https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement"
4747
],
4848
"brandlink": "index.html",
4949
"brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
@@ -62,5 +62,15 @@
6262
"brandlink": "index.html",
6363
"brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
6464
"primtype": null
65-
}
65+
},
66+
#{
67+
# "source": {"$import": "userguide-draft4-input.json"},
68+
# "target": "draft-4/UserGuide.html",
69+
# "renderlist": [],
70+
# "redirect": [],
71+
# "brandlink": "index.html",
72+
# "brandimg": "<img src='../CWL-Logo-Header.png' style='height: 61px; margin-top: -20px; margin-left: -20px'></img>",
73+
# "primtype": null
74+
#}
75+
6676
]

‎cwltool/schemas/site/draft3-deps.json

Lines changed: 135 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -2,75 +2,187 @@
22
{
33
"secondaryFiles": [
44
{
5+
"basename": "concepts.md",
56
"class": "File",
67
"location": "../draft-3/concepts.md"
78
},
89
{
9-
"entry": {
10-
"class": "Directory",
11-
"listing": [
12-
{
13-
"entry": {
10+
"basename": "salad",
11+
"location": "_:0600cfcc-4e4b-4213-a821-1009e8a44f5a",
12+
"class": "Directory",
13+
"listing": [
14+
{
15+
"basename": "schema_salad",
16+
"location": "_:1b18d943-4f8f-4c39-80ba-b30d2656d64e",
17+
"class": "Directory",
18+
"listing": [
19+
{
20+
"basename": "metaschema",
21+
"location": "_:ae5f64e3-e9d7-41db-b59e-97c1611182ee",
1422
"class": "Directory",
1523
"listing": [
1624
{
17-
"entry": {
18-
"class": "Directory",
19-
"listing": [
20-
{$import: draft3-metaschema.json}
21-
]
22-
},
23-
"entryname": "metaschema"
25+
"secondaryFiles": [
26+
{
27+
"secondaryFiles": [
28+
{
29+
"basename": "link_res_schema.yml",
30+
"class": "File",
31+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_schema.yml"
32+
},
33+
{
34+
"basename": "link_res_src.yml",
35+
"class": "File",
36+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_src.yml"
37+
},
38+
{
39+
"basename": "link_res_proc.yml",
40+
"class": "File",
41+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_proc.yml"
42+
}
43+
],
44+
"basename": "link_res.yml",
45+
"class": "File",
46+
"location": "../draft-3/salad/schema_salad/metaschema/link_res.yml"
47+
},
48+
{
49+
"basename": "salad.md",
50+
"class": "File",
51+
"location": "../draft-3/salad/schema_salad/metaschema/salad.md"
52+
},
53+
{
54+
"basename": "import_include.md",
55+
"class": "File",
56+
"location": "../draft-3/salad/schema_salad/metaschema/import_include.md"
57+
},
58+
{
59+
"secondaryFiles": [
60+
{
61+
"basename": "field_name_src.yml",
62+
"class": "File",
63+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_src.yml"
64+
},
65+
{
66+
"basename": "field_name_schema.yml",
67+
"class": "File",
68+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_schema.yml"
69+
},
70+
{
71+
"basename": "field_name_proc.yml",
72+
"class": "File",
73+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_proc.yml"
74+
}
75+
],
76+
"basename": "field_name.yml",
77+
"class": "File",
78+
"location": "../draft-3/salad/schema_salad/metaschema/field_name.yml"
79+
},
80+
{
81+
"secondaryFiles": [
82+
{
83+
"basename": "ident_res_proc.yml",
84+
"class": "File",
85+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_proc.yml"
86+
},
87+
{
88+
"basename": "ident_res_schema.yml",
89+
"class": "File",
90+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_schema.yml"
91+
},
92+
{
93+
"basename": "ident_res_src.yml",
94+
"class": "File",
95+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_src.yml"
96+
}
97+
],
98+
"basename": "ident_res.yml",
99+
"class": "File",
100+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res.yml"
101+
},
102+
{
103+
"secondaryFiles": [
104+
{
105+
"basename": "vocab_res_schema.yml",
106+
"class": "File",
107+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_schema.yml"
108+
},
109+
{
110+
"basename": "vocab_res_proc.yml",
111+
"class": "File",
112+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_proc.yml"
113+
},
114+
{
115+
"basename": "vocab_res_src.yml",
116+
"class": "File",
117+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_src.yml"
118+
}
119+
],
120+
"basename": "vocab_res.yml",
121+
"class": "File",
122+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res.yml"
123+
}
124+
],
125+
"basename": "metaschema.yml",
126+
"class": "File",
127+
"location": "../draft-3/salad/schema_salad/metaschema/metaschema.yml"
24128
}
25129
]
26-
},
27-
"entryname": "schema_salad"
28-
}
29-
]
30-
},
31-
"entryname": "salad"
130+
}
131+
]
132+
}
133+
]
32134
}
33135
],
136+
"basename": "Process.yml",
34137
"class": "File",
35138
"location": "../draft-3/Process.yml"
36139
},
37140
{
38141
"secondaryFiles": [
39142
{
143+
"basename": "contrib.md",
40144
"class": "File",
41145
"location": "../draft-3/contrib.md"
42146
},
43147
{
148+
"basename": "concepts.md",
44149
"class": "File",
45-
"location": "../draft-3/intro.md"
150+
"location": "../draft-3/concepts.md"
46151
},
47152
{
153+
"basename": "invocation.md",
48154
"class": "File",
49-
"location": "../draft-3/concepts.md"
155+
"location": "../draft-3/invocation.md"
50156
},
51157
{
158+
"basename": "intro.md",
52159
"class": "File",
53-
"location": "../draft-3/invocation.md"
160+
"location": "../draft-3/intro.md"
54161
}
55162
],
163+
"basename": "CommandLineTool.yml",
56164
"class": "File",
57165
"location": "../draft-3/CommandLineTool.yml"
58166
},
59167
{
60168
"secondaryFiles": [
61169
{
170+
"basename": "contrib.md",
62171
"class": "File",
63172
"location": "../draft-3/contrib.md"
64173
},
65174
{
175+
"basename": "concepts.md",
66176
"class": "File",
67-
"location": "../draft-3/intro.md"
177+
"location": "../draft-3/concepts.md"
68178
},
69179
{
180+
"basename": "intro.md",
70181
"class": "File",
71-
"location": "../draft-3/concepts.md"
182+
"location": "../draft-3/intro.md"
72183
}
73184
],
185+
"basename": "Workflow.yml",
74186
"class": "File",
75187
"location": "../draft-3/Workflow.yml"
76188
}

‎cwltool/schemas/site/draft3-metaschema.json

Lines changed: 104 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,104 @@
1+
{
2+
"secondaryFiles": [
3+
{
4+
"secondaryFiles": [
5+
{
6+
"basename": "link_res_schema.yml",
7+
"class": "File",
8+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_schema.yml"
9+
},
10+
{
11+
"basename": "link_res_src.yml",
12+
"class": "File",
13+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_src.yml"
14+
},
15+
{
16+
"basename": "link_res_proc.yml",
17+
"class": "File",
18+
"location": "../draft-3/salad/schema_salad/metaschema/link_res_proc.yml"
19+
}
20+
],
21+
"basename": "link_res.yml",
22+
"class": "File",
23+
"location": "../draft-3/salad/schema_salad/metaschema/link_res.yml"
24+
},
25+
{
26+
"basename": "salad.md",
27+
"class": "File",
28+
"location": "../draft-3/salad/schema_salad/metaschema/salad.md"
29+
},
30+
{
31+
"basename": "import_include.md",
32+
"class": "File",
33+
"location": "../draft-3/salad/schema_salad/metaschema/import_include.md"
34+
},
35+
{
36+
"secondaryFiles": [
37+
{
38+
"basename": "field_name_src.yml",
39+
"class": "File",
40+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_src.yml"
41+
},
42+
{
43+
"basename": "field_name_schema.yml",
44+
"class": "File",
45+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_schema.yml"
46+
},
47+
{
48+
"basename": "field_name_proc.yml",
49+
"class": "File",
50+
"location": "../draft-3/salad/schema_salad/metaschema/field_name_proc.yml"
51+
}
52+
],
53+
"basename": "field_name.yml",
54+
"class": "File",
55+
"location": "../draft-3/salad/schema_salad/metaschema/field_name.yml"
56+
},
57+
{
58+
"secondaryFiles": [
59+
{
60+
"basename": "ident_res_proc.yml",
61+
"class": "File",
62+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_proc.yml"
63+
},
64+
{
65+
"basename": "ident_res_schema.yml",
66+
"class": "File",
67+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_schema.yml"
68+
},
69+
{
70+
"basename": "ident_res_src.yml",
71+
"class": "File",
72+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res_src.yml"
73+
}
74+
],
75+
"basename": "ident_res.yml",
76+
"class": "File",
77+
"location": "../draft-3/salad/schema_salad/metaschema/ident_res.yml"
78+
},
79+
{
80+
"secondaryFiles": [
81+
{
82+
"basename": "vocab_res_schema.yml",
83+
"class": "File",
84+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_schema.yml"
85+
},
86+
{
87+
"basename": "vocab_res_proc.yml",
88+
"class": "File",
89+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_proc.yml"
90+
},
91+
{
92+
"basename": "vocab_res_src.yml",
93+
"class": "File",
94+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res_src.yml"
95+
}
96+
],
97+
"basename": "vocab_res.yml",
98+
"class": "File",
99+
"location": "../draft-3/salad/schema_salad/metaschema/vocab_res.yml"
100+
}
101+
],
102+
"class": "File",
103+
"location": "../draft-3/salad/schema_salad/metaschema/metaschema.yml"
104+
}

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